[ccp4bb] Problems in refinement with NCS and B-values

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: space group R3(R32) or H3(H32)?
From: Ricardo Aparicio aparicio {- at -} IQM {- dot -} UNICAMP {- dot -} BR
Date: 2007-07-06

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From: Celeste MacElrevey celeste_macelrevey {- at -} URMC {- dot -} ROCHESTER {- dot -} EDU
Date: 2007-07-06

Subject: Problems in refinement with NCS and B-values
From: ANA MARIA MISIC ammisic {- at -} WISC {- dot -} EDU
Date: 2007-07-06

Hello - I have nearly completed a crystal structure at 2.6 A resolution. There are 3 monomers per asymmetric unit (same protein in different conformations), and I have been using non-crystallographic symmetry during the refinement process (REFMAC5). I have been isotropically refining B-values and using TLS. My problem is that the B-values appear to be too tight as a result of non-crystallographic symmetry. For example, an Asp residue has well-defined density, and atomic B factors of about 40. However, the adjacent lysine, with no density for the side chain has B factors of 42. This does not make sense for them to have nearly identical B values, when there is differing density. This may be a consequence of having a residue with well defined density in chain A and chain B, but not chain C. When plotting residue number vs. B factor, the values seem to be too tightly grouped to make sense. Loosening NCS restraints leads to more variability in B factors, a lower R factor,
but higher R-free.

My question is how do I keep NCS, and allow B-factors to vary more so I have more reasonable values? I would appreciate any ideas you have. Thank you in advance for your time and assistance.

Ana M. Misic
Research Assistant
Department of Biomolecular Chemistry
Department of Bacteriology
University of Wisconsin - Madison
420 Henry Mall, Rm 230
Madison, WI 53706

Lab Phone: (608)265-9282
Fax: (608)262-9865

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: space group R3(R32) or H3(H32)?
From: Ricardo Aparicio aparicio {- at -} IQM {- dot -} UNICAMP {- dot -} BR
Date: 2007-07-06

Next message:
Subject: PDB-derived SF to map
From: Celeste MacElrevey celeste_macelrevey {- at -} URMC {- dot -} ROCHESTER {- dot -} EDU
Date: 2007-07-06